Starting phenix.real_space_refine on Wed Aug 5 13:56:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9umz_64333/08_2026/9umz_64333.cif Found real_map, /net/cci-nas-00/data/ceres_data/9umz_64333/08_2026/9umz_64333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9umz_64333/08_2026/9umz_64333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9umz_64333/08_2026/9umz_64333.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9umz_64333/08_2026/9umz_64333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9umz_64333/08_2026/9umz_64333.map" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 54 5.16 5 C 6294 2.51 5 N 1664 2.21 5 O 1978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10018 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1886 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 232} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1895 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "C" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1895 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "D" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1895 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "E" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1887 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "K" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 560 Classifications: {'RNA': 28} Modifications used: {'rna2p_pyr': 6, 'rna3p_pyr': 22} Link IDs: {'rna2p': 5, 'rna3p': 22} Time building chain proxies: 2.31, per 1000 atoms: 0.23 Number of scatterers: 10018 At special positions: 0 Unit cell: (71.25, 110.2, 120.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 28 15.00 O 1978 8.00 N 1664 7.00 C 6294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 146 " distance=2.04 Simple disulfide: pdb=" SG CYS E 116 " - pdb=" SG CYS E 146 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 349.0 milliseconds 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2298 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 0 sheets defined 74.3% alpha, 0.0% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 17 through 28 Processing helix chain 'A' and resid 34 through 46 removed outlier: 3.688A pdb=" N ILE A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU A 42 " --> pdb=" O ILE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 64 removed outlier: 3.659A pdb=" N LYS A 55 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 75 removed outlier: 3.641A pdb=" N GLY A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.569A pdb=" N ARG A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.550A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 removed outlier: 4.378A pdb=" N ALA A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 147 through 152 removed outlier: 4.101A pdb=" N GLY A 150 " --> pdb=" O MET A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 182 removed outlier: 3.585A pdb=" N TRP A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 197 through 206 removed outlier: 3.623A pdb=" N LEU A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.975A pdb=" N ARG A 215 " --> pdb=" O PRO A 211 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 removed outlier: 3.552A pdb=" N GLU A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 4.094A pdb=" N PHE B 11 " --> pdb=" O ILE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 22 through 27 removed outlier: 3.702A pdb=" N ARG B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 22 through 27' Processing helix chain 'B' and resid 36 through 47 removed outlier: 3.632A pdb=" N LYS B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 64 removed outlier: 3.710A pdb=" N LYS B 55 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 73 Processing helix chain 'B' and resid 76 through 91 Processing helix chain 'B' and resid 103 through 110 removed outlier: 3.575A pdb=" N ALA B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 removed outlier: 3.586A pdb=" N THR B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.851A pdb=" N MET B 145 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 159 through 182 removed outlier: 4.191A pdb=" N TRP B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 174 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 207 removed outlier: 3.960A pdb=" N PHE B 197 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Proline residue: B 200 - end of helix removed outlier: 3.510A pdb=" N ALA B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.613A pdb=" N LYS B 217 " --> pdb=" O ASP B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 removed outlier: 3.680A pdb=" N GLU B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.726A pdb=" N ARG C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 29 Processing helix chain 'C' and resid 34 through 46 removed outlier: 3.561A pdb=" N THR C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 64 removed outlier: 4.240A pdb=" N VAL C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 60 " --> pdb=" O PHE C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 76 through 91 removed outlier: 4.034A pdb=" N ARG C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 111 removed outlier: 3.639A pdb=" N LEU C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 removed outlier: 3.529A pdb=" N ALA C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 141 through 145 Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 159 through 182 removed outlier: 3.903A pdb=" N TRP C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 186 removed outlier: 3.550A pdb=" N ARG C 186 " --> pdb=" O VAL C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 186' Processing helix chain 'C' and resid 189 through 197 removed outlier: 3.653A pdb=" N ASN C 195 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C 197 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 206 Processing helix chain 'C' and resid 211 through 222 removed outlier: 3.592A pdb=" N ARG C 215 " --> pdb=" O PRO C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 244 removed outlier: 4.079A pdb=" N GLU C 236 " --> pdb=" O SER C 232 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 14 removed outlier: 3.735A pdb=" N ARG D 6 " --> pdb=" O SER D 2 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 10 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN D 14 " --> pdb=" O GLU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 34 through 47 removed outlier: 3.515A pdb=" N LEU D 42 " --> pdb=" O ILE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 64 removed outlier: 4.162A pdb=" N LYS D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE D 56 " --> pdb=" O LYS D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.778A pdb=" N GLY D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 103 through 111 Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'D' and resid 123 through 126 removed outlier: 3.721A pdb=" N LEU D 126 " --> pdb=" O LYS D 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 123 through 126' Processing helix chain 'D' and resid 129 through 137 removed outlier: 3.652A pdb=" N LEU D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 153 removed outlier: 3.602A pdb=" N PHE D 149 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 150 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER D 151 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 182 removed outlier: 3.641A pdb=" N THR D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP D 173 " --> pdb=" O ALA D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 206 removed outlier: 3.966A pdb=" N PHE D 197 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) Proline residue: D 200 - end of helix Processing helix chain 'D' and resid 211 through 222 removed outlier: 3.700A pdb=" N LYS D 217 " --> pdb=" O ASP D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 244 removed outlier: 3.609A pdb=" N ASN D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 14 removed outlier: 3.700A pdb=" N ALA E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN E 14 " --> pdb=" O GLU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 29 removed outlier: 3.552A pdb=" N GLU E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 46 removed outlier: 3.514A pdb=" N ILE E 38 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 64 removed outlier: 3.963A pdb=" N LYS E 55 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 73 removed outlier: 3.557A pdb=" N GLY E 73 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 91 removed outlier: 3.701A pdb=" N ARG E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 111 through 122 removed outlier: 3.588A pdb=" N ALA E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA E 120 " --> pdb=" O CYS E 116 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA E 121 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 141 through 145 removed outlier: 3.549A pdb=" N MET E 144 " --> pdb=" O PRO E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 159 through 182 removed outlier: 3.715A pdb=" N LEU E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP E 173 " --> pdb=" O ALA E 169 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN E 174 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 196 Processing helix chain 'E' and resid 197 through 207 removed outlier: 3.512A pdb=" N ALA E 203 " --> pdb=" O ASP E 199 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA E 204 " --> pdb=" O PRO E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 222 removed outlier: 3.588A pdb=" N VAL E 216 " --> pdb=" O ASN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 244 removed outlier: 3.663A pdb=" N GLU E 236 " --> pdb=" O SER E 232 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN E 244 " --> pdb=" O ALA E 240 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3069 1.34 - 1.46: 1603 1.46 - 1.58: 5436 1.58 - 1.70: 55 1.70 - 1.82: 98 Bond restraints: 10261 Sorted by residual: bond pdb=" CA GLU B 31 " pdb=" CB GLU B 31 " ideal model delta sigma weight residual 1.526 1.556 -0.030 1.70e-02 3.46e+03 3.15e+00 bond pdb=" CG ARG B 26 " pdb=" CD ARG B 26 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CB GLU E 88 " pdb=" CG GLU E 88 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.20e-01 bond pdb=" CB GLN D 87 " pdb=" CG GLN D 87 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.74e-01 bond pdb=" C GLY D 79 " pdb=" O GLY D 79 " ideal model delta sigma weight residual 1.239 1.245 -0.006 7.10e-03 1.98e+04 7.71e-01 ... (remaining 10256 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 13673 1.75 - 3.50: 279 3.50 - 5.25: 41 5.25 - 7.00: 8 7.00 - 8.74: 6 Bond angle restraints: 14007 Sorted by residual: angle pdb=" O5' U K 26 " pdb=" C5' U K 26 " pdb=" C4' U K 26 " ideal model delta sigma weight residual 109.40 112.17 -2.77 8.00e-01 1.56e+00 1.20e+01 angle pdb=" O5' U K 25 " pdb=" C5' U K 25 " pdb=" C4' U K 25 " ideal model delta sigma weight residual 109.40 112.06 -2.66 8.00e-01 1.56e+00 1.10e+01 angle pdb=" O5' U K 5 " pdb=" C5' U K 5 " pdb=" C4' U K 5 " ideal model delta sigma weight residual 109.40 112.03 -2.63 8.00e-01 1.56e+00 1.08e+01 angle pdb=" O5' U K 17 " pdb=" C5' U K 17 " pdb=" C4' U K 17 " ideal model delta sigma weight residual 109.40 112.02 -2.62 8.00e-01 1.56e+00 1.07e+01 angle pdb=" O5' U K 7 " pdb=" C5' U K 7 " pdb=" C4' U K 7 " ideal model delta sigma weight residual 109.40 112.01 -2.61 8.00e-01 1.56e+00 1.06e+01 ... (remaining 14002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5651 17.96 - 35.92: 523 35.92 - 53.88: 104 53.88 - 71.84: 44 71.84 - 89.81: 11 Dihedral angle restraints: 6333 sinusoidal: 2781 harmonic: 3552 Sorted by residual: dihedral pdb=" CA TYR B 30 " pdb=" C TYR B 30 " pdb=" N GLU B 31 " pdb=" CA GLU B 31 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP E 34 " pdb=" CB ASP E 34 " pdb=" CG ASP E 34 " pdb=" OD1 ASP E 34 " ideal model delta sinusoidal sigma weight residual -30.00 -91.00 61.00 1 2.00e+01 2.50e-03 1.24e+01 dihedral pdb=" CB GLU D 20 " pdb=" CG GLU D 20 " pdb=" CD GLU D 20 " pdb=" OE1 GLU D 20 " ideal model delta sinusoidal sigma weight residual 0.00 88.34 -88.34 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 6330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1392 0.057 - 0.114: 196 0.114 - 0.171: 35 0.171 - 0.228: 0 0.228 - 0.285: 1 Chirality restraints: 1624 Sorted by residual: chirality pdb=" CB ILE A 102 " pdb=" CA ILE A 102 " pdb=" CG1 ILE A 102 " pdb=" CG2 ILE A 102 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2' U K 18 " pdb=" C3' U K 18 " pdb=" O2' U K 18 " pdb=" C1' U K 18 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" C2' U K 23 " pdb=" C3' U K 23 " pdb=" O2' U K 23 " pdb=" C1' U K 23 " both_signs ideal model delta sigma weight residual False -2.62 -2.75 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1621 not shown) Planarity restraints: 1686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 141 " 0.029 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO C 142 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 26 " -0.123 9.50e-02 1.11e+02 5.55e-02 2.52e+00 pdb=" NE ARG B 26 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 26 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 26 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 26 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 111 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO E 112 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 112 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 112 " -0.022 5.00e-02 4.00e+02 ... (remaining 1683 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 174 2.67 - 3.23: 10148 3.23 - 3.79: 15803 3.79 - 4.34: 20710 4.34 - 4.90: 32153 Nonbonded interactions: 78988 Sorted by model distance: nonbonded pdb=" O LEU C 28 " pdb=" NH2 ARG D 64 " model vdw 2.114 3.120 nonbonded pdb=" OE2 GLU A 27 " pdb=" OG SER B 78 " model vdw 2.173 3.040 nonbonded pdb=" OD2 ASP C 199 " pdb=" O2' U K 15 " model vdw 2.189 3.040 nonbonded pdb=" O THR D 98 " pdb=" OG SER D 101 " model vdw 2.219 3.040 nonbonded pdb=" O SER E 159 " pdb=" OG1 THR E 162 " model vdw 2.237 3.040 ... (remaining 78983 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 245) selection = (chain 'B' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 245)) selection = (chain 'C' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 245)) selection = (chain 'D' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 245)) selection = (chain 'E' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 245)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.970 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10263 Z= 0.111 Angle : 0.596 8.745 14011 Z= 0.320 Chirality : 0.041 0.285 1624 Planarity : 0.004 0.056 1686 Dihedral : 15.104 89.806 4029 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.23), residues: 1214 helix: -0.49 (0.18), residues: 745 sheet: None (None), residues: 0 loop : 0.38 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 26 TYR 0.021 0.001 TYR B 170 PHE 0.023 0.002 PHE E 197 TRP 0.023 0.002 TRP C 114 HIS 0.001 0.000 HIS D 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (10261) covalent geometry : angle 0.59548 / 0.32 (14007) SS BOND : bond 0.00306 / 0.16 ( 2) SS BOND : angle 1.16625 / 0.63 ( 4) hydrogen bonds : bond 0.29379 / 18.59 ( 496) hydrogen bonds : angle 8.06804 / 5.60 ( 1434) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7960 (tpp80) REVERT: B 134 ASN cc_start: 0.8791 (m110) cc_final: 0.8579 (m-40) REVERT: E 144 MET cc_start: 0.7805 (ppp) cc_final: 0.7318 (ppp) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.0781 time to fit residues: 27.2542 Evaluate side-chains 199 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN A 244 ASN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 HIS C 212 ASN ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.182770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.154364 restraints weight = 16853.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.159083 restraints weight = 10485.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.162491 restraints weight = 7406.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.164942 restraints weight = 5671.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.166725 restraints weight = 4610.618| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10263 Z= 0.155 Angle : 0.633 8.591 14011 Z= 0.331 Chirality : 0.042 0.159 1624 Planarity : 0.005 0.044 1686 Dihedral : 12.229 75.809 1759 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.70 % Allowed : 12.32 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.23), residues: 1214 helix: -0.35 (0.17), residues: 788 sheet: None (None), residues: 0 loop : 0.13 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 26 TYR 0.016 0.002 TYR A 194 PHE 0.026 0.002 PHE B 11 TRP 0.019 0.002 TRP D 50 HIS 0.002 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (10261) covalent geometry : angle 0.63269 / 0.33 (14007) SS BOND : bond 0.00400 / 0.21 ( 2) SS BOND : angle 1.67157 / 0.93 ( 4) hydrogen bonds : bond 0.05352 / 3.41 ( 496) hydrogen bonds : angle 5.33966 / 3.70 ( 1434) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7338 (ttm) cc_final: 0.7078 (ttm) REVERT: B 17 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.7360 (p0) REVERT: B 116 CYS cc_start: 0.7542 (m) cc_final: 0.7322 (m) REVERT: B 134 ASN cc_start: 0.8809 (m110) cc_final: 0.8572 (m-40) REVERT: B 174 GLN cc_start: 0.8568 (mp10) cc_final: 0.8324 (mp10) REVERT: C 17 ASN cc_start: 0.8577 (t0) cc_final: 0.8278 (t0) REVERT: E 144 MET cc_start: 0.7877 (ppp) cc_final: 0.7153 (ppp) outliers start: 17 outliers final: 5 residues processed: 225 average time/residue: 0.0770 time to fit residues: 24.6912 Evaluate side-chains 201 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain C residue 193 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 21 optimal weight: 0.0470 chunk 31 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 overall best weight: 3.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN D 182 ASN ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.158768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.128559 restraints weight = 16937.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.132892 restraints weight = 10880.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.135994 restraints weight = 7903.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138175 restraints weight = 6225.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.139868 restraints weight = 5196.918| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 10263 Z= 0.269 Angle : 0.731 10.022 14011 Z= 0.379 Chirality : 0.047 0.186 1624 Planarity : 0.005 0.054 1686 Dihedral : 12.658 80.682 1759 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.21 % Allowed : 15.83 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.23), residues: 1214 helix: -0.36 (0.17), residues: 782 sheet: None (None), residues: 0 loop : -0.01 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 95 TYR 0.021 0.003 TYR A 194 PHE 0.022 0.003 PHE B 210 TRP 0.020 0.002 TRP D 114 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.27 (10261) covalent geometry : angle 0.73085 / 0.38 (14007) SS BOND : bond 0.00580 / 0.30 ( 2) SS BOND : angle 1.81964 / 0.99 ( 4) hydrogen bonds : bond 0.05088 / 3.23 ( 496) hydrogen bonds : angle 5.36679 / 3.68 ( 1434) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.8307 (t80) cc_final: 0.7824 (t80) REVERT: A 144 MET cc_start: 0.7359 (ttm) cc_final: 0.6776 (ttm) REVERT: A 195 ASN cc_start: 0.8343 (m110) cc_final: 0.8055 (m110) REVERT: A 217 LYS cc_start: 0.9021 (pttm) cc_final: 0.8733 (pttp) REVERT: B 75 MET cc_start: 0.4844 (ptm) cc_final: 0.4610 (ptm) REVERT: B 88 GLU cc_start: 0.8093 (tt0) cc_final: 0.7883 (tm-30) REVERT: B 134 ASN cc_start: 0.8900 (m110) cc_final: 0.8634 (m-40) REVERT: B 170 TYR cc_start: 0.7963 (t80) cc_final: 0.7480 (t80) REVERT: B 174 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8209 (mp10) REVERT: C 17 ASN cc_start: 0.8688 (t0) cc_final: 0.8364 (t0) REVERT: C 26 ARG cc_start: 0.8860 (mtm180) cc_final: 0.8638 (ttp-110) REVERT: C 133 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7006 (ttp) REVERT: C 213 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8294 (p0) REVERT: D 147 MET cc_start: 0.8368 (tpt) cc_final: 0.7811 (tpt) REVERT: E 144 MET cc_start: 0.7879 (ppp) cc_final: 0.6989 (ppp) REVERT: E 220 LYS cc_start: 0.8140 (mmtp) cc_final: 0.7866 (mmtp) REVERT: E 242 TYR cc_start: 0.7597 (t80) cc_final: 0.7246 (t80) outliers start: 42 outliers final: 25 residues processed: 237 average time/residue: 0.0733 time to fit residues: 25.6665 Evaluate side-chains 226 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 193 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.4980 chunk 95 optimal weight: 30.0000 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 17 ASN B 212 ASN D 182 ASN ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.171287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.141023 restraints weight = 16739.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.145873 restraints weight = 10447.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.149342 restraints weight = 7407.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.151879 restraints weight = 5702.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.153612 restraints weight = 4647.968| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10263 Z= 0.134 Angle : 0.613 11.280 14011 Z= 0.311 Chirality : 0.041 0.178 1624 Planarity : 0.004 0.050 1686 Dihedral : 12.530 81.672 1759 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.51 % Allowed : 20.64 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.23), residues: 1214 helix: -0.18 (0.18), residues: 785 sheet: None (None), residues: 0 loop : -0.01 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 233 TYR 0.022 0.002 TYR A 194 PHE 0.030 0.002 PHE B 60 TRP 0.029 0.002 TRP E 173 HIS 0.001 0.001 HIS E 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (10261) covalent geometry : angle 0.61221 / 0.31 (14007) SS BOND : bond 0.00571 / 0.28 ( 2) SS BOND : angle 1.44718 / 0.78 ( 4) hydrogen bonds : bond 0.04162 / 2.66 ( 496) hydrogen bonds : angle 4.93395 / 3.39 ( 1434) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7449 (ttm) cc_final: 0.6682 (ttm) REVERT: A 194 TYR cc_start: 0.6845 (t80) cc_final: 0.6498 (t80) REVERT: A 195 ASN cc_start: 0.8287 (m-40) cc_final: 0.7114 (m-40) REVERT: A 217 LYS cc_start: 0.9005 (pttm) cc_final: 0.8682 (pttp) REVERT: B 88 GLU cc_start: 0.8119 (tt0) cc_final: 0.7886 (tm-30) REVERT: B 134 ASN cc_start: 0.8800 (m110) cc_final: 0.8481 (m-40) REVERT: B 174 GLN cc_start: 0.8603 (mp10) cc_final: 0.8212 (mp10) REVERT: C 17 ASN cc_start: 0.8595 (t0) cc_final: 0.8290 (t0) REVERT: C 26 ARG cc_start: 0.8820 (mtm180) cc_final: 0.8587 (ttp-110) REVERT: C 219 LEU cc_start: 0.8753 (mt) cc_final: 0.8537 (mt) REVERT: D 100 LEU cc_start: 0.8396 (tp) cc_final: 0.8025 (tt) REVERT: D 133 MET cc_start: 0.8119 (mmm) cc_final: 0.7914 (mmm) REVERT: E 144 MET cc_start: 0.7945 (ppp) cc_final: 0.6901 (ppp) REVERT: E 168 GLU cc_start: 0.8867 (tp30) cc_final: 0.8596 (tp30) REVERT: E 174 GLN cc_start: 0.7645 (tt0) cc_final: 0.7303 (pp30) REVERT: E 197 PHE cc_start: 0.7135 (t80) cc_final: 0.6815 (t80) REVERT: E 220 LYS cc_start: 0.7848 (mmtp) cc_final: 0.7613 (mmtp) REVERT: E 242 TYR cc_start: 0.7660 (t80) cc_final: 0.7091 (t80) outliers start: 25 outliers final: 17 residues processed: 234 average time/residue: 0.0757 time to fit residues: 25.7532 Evaluate side-chains 220 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 42 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 0.0370 chunk 49 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 57 optimal weight: 0.0370 chunk 80 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.169328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.138808 restraints weight = 16795.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.143455 restraints weight = 10588.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.146762 restraints weight = 7593.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.149204 restraints weight = 5929.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.150822 restraints weight = 4875.701| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10263 Z= 0.163 Angle : 0.638 11.102 14011 Z= 0.321 Chirality : 0.042 0.180 1624 Planarity : 0.005 0.135 1686 Dihedral : 12.579 82.844 1759 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.81 % Allowed : 22.14 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.23), residues: 1214 helix: -0.14 (0.18), residues: 793 sheet: None (None), residues: 0 loop : -0.07 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 106 TYR 0.044 0.002 TYR A 194 PHE 0.023 0.002 PHE B 60 TRP 0.019 0.002 TRP E 50 HIS 0.002 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (10261) covalent geometry : angle 0.63749 / 0.32 (14007) SS BOND : bond 0.00327 / 0.17 ( 2) SS BOND : angle 1.35634 / 0.76 ( 4) hydrogen bonds : bond 0.04062 / 2.60 ( 496) hydrogen bonds : angle 4.90586 / 3.36 ( 1434) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.8118 (t80) cc_final: 0.7490 (t80) REVERT: A 144 MET cc_start: 0.7593 (ttm) cc_final: 0.6763 (ttm) REVERT: A 185 MET cc_start: 0.8671 (mmt) cc_final: 0.8432 (mpp) REVERT: A 210 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: A 217 LYS cc_start: 0.9004 (pttm) cc_final: 0.8705 (pttp) REVERT: B 134 ASN cc_start: 0.8828 (m110) cc_final: 0.8506 (m-40) REVERT: C 26 ARG cc_start: 0.8838 (mtm180) cc_final: 0.8581 (ttp-110) REVERT: C 81 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8431 (mtmm) REVERT: C 133 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7268 (ttp) REVERT: C 170 TYR cc_start: 0.8392 (t80) cc_final: 0.8005 (t80) REVERT: D 100 LEU cc_start: 0.8397 (tp) cc_final: 0.8008 (tt) REVERT: D 125 TYR cc_start: 0.7930 (m-80) cc_final: 0.7567 (m-80) REVERT: E 144 MET cc_start: 0.7995 (ppp) cc_final: 0.7114 (ppp) REVERT: E 168 GLU cc_start: 0.8903 (tp30) cc_final: 0.8537 (tp30) REVERT: E 220 LYS cc_start: 0.7764 (mmtp) cc_final: 0.7529 (mmtp) REVERT: E 242 TYR cc_start: 0.7707 (t80) cc_final: 0.7127 (t80) outliers start: 28 outliers final: 20 residues processed: 225 average time/residue: 0.0716 time to fit residues: 23.7598 Evaluate side-chains 219 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 134 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.167851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.138234 restraints weight = 16857.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.142954 restraints weight = 10462.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.146335 restraints weight = 7382.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148542 restraints weight = 5685.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.150409 restraints weight = 4695.460| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10263 Z= 0.167 Angle : 0.640 11.328 14011 Z= 0.323 Chirality : 0.041 0.184 1624 Planarity : 0.004 0.051 1686 Dihedral : 12.603 83.663 1759 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.31 % Allowed : 23.35 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.23), residues: 1214 helix: -0.13 (0.18), residues: 797 sheet: None (None), residues: 0 loop : -0.03 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 233 TYR 0.015 0.002 TYR E 30 PHE 0.031 0.002 PHE E 197 TRP 0.021 0.002 TRP E 50 HIS 0.002 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (10261) covalent geometry : angle 0.63936 / 0.32 (14007) SS BOND : bond 0.00357 / 0.18 ( 2) SS BOND : angle 2.01741 / 1.07 ( 4) hydrogen bonds : bond 0.03972 / 2.54 ( 496) hydrogen bonds : angle 4.87816 / 3.35 ( 1434) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.8149 (t80) cc_final: 0.7571 (t80) REVERT: A 144 MET cc_start: 0.7477 (ttm) cc_final: 0.6699 (ttm) REVERT: A 185 MET cc_start: 0.8697 (mmt) cc_final: 0.8432 (mpp) REVERT: A 210 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.6737 (m-80) REVERT: A 217 LYS cc_start: 0.8996 (pttm) cc_final: 0.8702 (pttp) REVERT: B 134 ASN cc_start: 0.8817 (m110) cc_final: 0.8503 (m-40) REVERT: C 26 ARG cc_start: 0.8815 (mtm180) cc_final: 0.8577 (ttp-110) REVERT: C 81 LYS cc_start: 0.8713 (mtmm) cc_final: 0.8457 (mtmm) REVERT: C 133 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7308 (ttp) REVERT: C 170 TYR cc_start: 0.8483 (t80) cc_final: 0.8136 (t80) REVERT: C 185 MET cc_start: 0.8123 (tpt) cc_final: 0.7782 (tpt) REVERT: D 100 LEU cc_start: 0.8393 (tp) cc_final: 0.7983 (tt) REVERT: D 126 LEU cc_start: 0.8988 (mp) cc_final: 0.8780 (mp) REVERT: D 133 MET cc_start: 0.8141 (mmm) cc_final: 0.7913 (mmm) REVERT: E 75 MET cc_start: 0.5731 (OUTLIER) cc_final: 0.5064 (ttt) REVERT: E 144 MET cc_start: 0.7978 (ppp) cc_final: 0.7152 (ppp) REVERT: E 168 GLU cc_start: 0.8925 (tp30) cc_final: 0.8451 (tp30) REVERT: E 210 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: E 242 TYR cc_start: 0.7564 (t80) cc_final: 0.6862 (t80) outliers start: 33 outliers final: 24 residues processed: 230 average time/residue: 0.0710 time to fit residues: 24.3576 Evaluate side-chains 222 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 210 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 GLN ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN E 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.169856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.139957 restraints weight = 16715.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.144685 restraints weight = 10455.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.148039 restraints weight = 7415.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.150506 restraints weight = 5730.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.152069 restraints weight = 4691.418| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10263 Z= 0.144 Angle : 0.626 11.784 14011 Z= 0.316 Chirality : 0.041 0.174 1624 Planarity : 0.004 0.051 1686 Dihedral : 12.590 85.258 1759 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.91 % Allowed : 24.15 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1214 helix: -0.05 (0.18), residues: 791 sheet: None (None), residues: 0 loop : -0.04 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 6 TYR 0.017 0.002 TYR D 125 PHE 0.031 0.002 PHE D 149 TRP 0.021 0.002 TRP E 50 HIS 0.001 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (10261) covalent geometry : angle 0.62512 / 0.32 (14007) SS BOND : bond 0.00277 / 0.14 ( 2) SS BOND : angle 1.77900 / 0.94 ( 4) hydrogen bonds : bond 0.03795 / 2.43 ( 496) hydrogen bonds : angle 4.79364 / 3.29 ( 1434) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.7561 (OUTLIER) cc_final: 0.6946 (p) REVERT: A 140 TYR cc_start: 0.8093 (t80) cc_final: 0.7302 (t80) REVERT: A 144 MET cc_start: 0.7428 (ttm) cc_final: 0.6372 (ttm) REVERT: A 185 MET cc_start: 0.8694 (mmt) cc_final: 0.8440 (mpp) REVERT: A 210 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.6746 (m-80) REVERT: A 217 LYS cc_start: 0.9008 (pttm) cc_final: 0.8739 (pttp) REVERT: B 134 ASN cc_start: 0.8706 (m110) cc_final: 0.8377 (m-40) REVERT: C 26 ARG cc_start: 0.8798 (mtm180) cc_final: 0.8520 (ttp-110) REVERT: C 133 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7396 (ttp) REVERT: C 170 TYR cc_start: 0.8490 (t80) cc_final: 0.8181 (t80) REVERT: D 100 LEU cc_start: 0.8379 (tp) cc_final: 0.7963 (tt) REVERT: D 126 LEU cc_start: 0.8937 (mp) cc_final: 0.8695 (mp) REVERT: E 75 MET cc_start: 0.5606 (OUTLIER) cc_final: 0.5002 (ttt) REVERT: E 144 MET cc_start: 0.8039 (ppp) cc_final: 0.7194 (ppp) REVERT: E 168 GLU cc_start: 0.8935 (tp30) cc_final: 0.8640 (tp30) REVERT: E 210 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: E 242 TYR cc_start: 0.7549 (t80) cc_final: 0.6941 (t80) outliers start: 39 outliers final: 25 residues processed: 232 average time/residue: 0.0706 time to fit residues: 24.1106 Evaluate side-chains 226 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 212 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 76 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.169665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.139986 restraints weight = 16630.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.144710 restraints weight = 10380.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.148076 restraints weight = 7335.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.150464 restraints weight = 5651.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.152196 restraints weight = 4637.647| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10263 Z= 0.149 Angle : 0.635 11.525 14011 Z= 0.321 Chirality : 0.041 0.187 1624 Planarity : 0.004 0.051 1686 Dihedral : 12.588 86.156 1759 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.91 % Allowed : 25.05 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1214 helix: -0.07 (0.18), residues: 793 sheet: None (None), residues: 0 loop : 0.01 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 233 TYR 0.024 0.002 TYR A 194 PHE 0.029 0.002 PHE E 209 TRP 0.026 0.002 TRP D 50 HIS 0.002 0.001 HIS E 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (10261) covalent geometry : angle 0.63440 / 0.32 (14007) SS BOND : bond 0.00284 / 0.14 ( 2) SS BOND : angle 1.74168 / 0.94 ( 4) hydrogen bonds : bond 0.03813 / 2.44 ( 496) hydrogen bonds : angle 4.80711 / 3.30 ( 1434) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.7578 (OUTLIER) cc_final: 0.6968 (p) REVERT: A 140 TYR cc_start: 0.8085 (t80) cc_final: 0.7325 (t80) REVERT: A 144 MET cc_start: 0.7438 (ttm) cc_final: 0.6323 (ttm) REVERT: A 210 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6745 (m-80) REVERT: A 217 LYS cc_start: 0.9020 (pttm) cc_final: 0.8729 (pttp) REVERT: B 134 ASN cc_start: 0.8666 (m110) cc_final: 0.8368 (m-40) REVERT: C 26 ARG cc_start: 0.8793 (mtm180) cc_final: 0.8473 (ttp-110) REVERT: C 81 LYS cc_start: 0.8629 (mttp) cc_final: 0.8407 (mtmm) REVERT: C 133 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7470 (ttp) REVERT: C 170 TYR cc_start: 0.8501 (t80) cc_final: 0.8215 (t80) REVERT: C 219 LEU cc_start: 0.8895 (mt) cc_final: 0.8618 (mt) REVERT: D 100 LEU cc_start: 0.8343 (tp) cc_final: 0.7926 (tt) REVERT: D 133 MET cc_start: 0.8099 (mmm) cc_final: 0.7809 (mmm) REVERT: E 75 MET cc_start: 0.5489 (ttt) cc_final: 0.4831 (ttt) REVERT: E 144 MET cc_start: 0.8084 (ppp) cc_final: 0.7420 (ppp) REVERT: E 168 GLU cc_start: 0.8885 (tp30) cc_final: 0.8614 (tp30) REVERT: E 220 LYS cc_start: 0.7849 (mmtp) cc_final: 0.7632 (mmtp) REVERT: E 242 TYR cc_start: 0.7530 (t80) cc_final: 0.6922 (t80) outliers start: 29 outliers final: 23 residues processed: 226 average time/residue: 0.0679 time to fit residues: 22.8477 Evaluate side-chains 221 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 11 PHE Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 212 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 27 optimal weight: 0.0170 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN E 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.172324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.143273 restraints weight = 16541.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.147949 restraints weight = 10295.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.151290 restraints weight = 7264.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.153442 restraints weight = 5582.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.155288 restraints weight = 4608.397| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10263 Z= 0.129 Angle : 0.651 13.133 14011 Z= 0.322 Chirality : 0.040 0.195 1624 Planarity : 0.004 0.051 1686 Dihedral : 12.567 87.200 1759 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.91 % Allowed : 25.25 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.24), residues: 1214 helix: -0.03 (0.18), residues: 792 sheet: None (None), residues: 0 loop : -0.04 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 233 TYR 0.024 0.002 TYR A 194 PHE 0.026 0.002 PHE E 197 TRP 0.029 0.002 TRP D 50 HIS 0.001 0.000 HIS E 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (10261) covalent geometry : angle 0.65086 / 0.32 (14007) SS BOND : bond 0.00286 / 0.14 ( 2) SS BOND : angle 1.76927 / 0.94 ( 4) hydrogen bonds : bond 0.03715 / 2.36 ( 496) hydrogen bonds : angle 4.71771 / 3.24 ( 1434) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.7514 (OUTLIER) cc_final: 0.6919 (p) REVERT: A 140 TYR cc_start: 0.8017 (t80) cc_final: 0.7274 (t80) REVERT: A 144 MET cc_start: 0.7418 (ttm) cc_final: 0.6371 (ttm) REVERT: A 147 MET cc_start: 0.8154 (tpt) cc_final: 0.7879 (tpt) REVERT: A 210 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.6727 (m-80) REVERT: A 217 LYS cc_start: 0.8981 (pttm) cc_final: 0.8705 (pttp) REVERT: B 134 ASN cc_start: 0.8695 (m110) cc_final: 0.8387 (m-40) REVERT: C 26 ARG cc_start: 0.8806 (mtm180) cc_final: 0.8480 (ttp-110) REVERT: C 81 LYS cc_start: 0.8579 (mttp) cc_final: 0.8352 (mtmm) REVERT: C 133 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7539 (ttp) REVERT: C 170 TYR cc_start: 0.8450 (t80) cc_final: 0.8183 (t80) REVERT: C 219 LEU cc_start: 0.8924 (mt) cc_final: 0.8632 (mt) REVERT: D 100 LEU cc_start: 0.8296 (tp) cc_final: 0.7852 (tt) REVERT: D 197 PHE cc_start: 0.7778 (p90) cc_final: 0.7561 (p90) REVERT: E 75 MET cc_start: 0.5243 (OUTLIER) cc_final: 0.4506 (ttt) REVERT: E 144 MET cc_start: 0.7918 (ppp) cc_final: 0.7340 (ppp) REVERT: E 168 GLU cc_start: 0.8862 (tp30) cc_final: 0.8334 (tp30) REVERT: E 242 TYR cc_start: 0.7520 (t80) cc_final: 0.6748 (t80) outliers start: 29 outliers final: 24 residues processed: 224 average time/residue: 0.0666 time to fit residues: 22.2451 Evaluate side-chains 218 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 212 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.0000 chunk 29 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.168187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137873 restraints weight = 16741.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.142547 restraints weight = 10519.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.145818 restraints weight = 7510.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.148162 restraints weight = 5858.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.149762 restraints weight = 4846.036| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10263 Z= 0.191 Angle : 0.710 12.644 14011 Z= 0.353 Chirality : 0.043 0.289 1624 Planarity : 0.005 0.052 1686 Dihedral : 12.640 87.331 1759 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.21 % Allowed : 26.15 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.24), residues: 1214 helix: -0.07 (0.18), residues: 787 sheet: None (None), residues: 0 loop : -0.12 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 233 TYR 0.025 0.002 TYR A 194 PHE 0.027 0.003 PHE A 11 TRP 0.027 0.002 TRP E 4 HIS 0.002 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (10261) covalent geometry : angle 0.70879 / 0.35 (14007) SS BOND : bond 0.00280 / 0.14 ( 2) SS BOND : angle 2.02931 / 1.09 ( 4) hydrogen bonds : bond 0.03945 / 2.50 ( 496) hydrogen bonds : angle 4.85859 / 3.34 ( 1434) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.7660 (OUTLIER) cc_final: 0.7032 (p) REVERT: A 140 TYR cc_start: 0.8123 (t80) cc_final: 0.7511 (t80) REVERT: A 144 MET cc_start: 0.7514 (ttm) cc_final: 0.6680 (ttm) REVERT: A 210 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.6752 (m-80) REVERT: A 217 LYS cc_start: 0.9026 (pttm) cc_final: 0.8726 (pttp) REVERT: B 134 ASN cc_start: 0.8836 (m110) cc_final: 0.8544 (m-40) REVERT: C 26 ARG cc_start: 0.8839 (mtm180) cc_final: 0.8533 (ttp-110) REVERT: C 81 LYS cc_start: 0.8642 (mttp) cc_final: 0.8438 (mtmm) REVERT: C 133 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7439 (ttp) REVERT: C 170 TYR cc_start: 0.8537 (t80) cc_final: 0.8320 (t80) REVERT: C 219 LEU cc_start: 0.8948 (mt) cc_final: 0.8662 (mt) REVERT: D 100 LEU cc_start: 0.8371 (tp) cc_final: 0.7953 (tt) REVERT: D 144 MET cc_start: 0.5409 (tmm) cc_final: 0.4443 (tmm) REVERT: E 75 MET cc_start: 0.5857 (OUTLIER) cc_final: 0.5186 (ttt) REVERT: E 144 MET cc_start: 0.8038 (ppp) cc_final: 0.7435 (ppp) REVERT: E 168 GLU cc_start: 0.8945 (tp30) cc_final: 0.8402 (tp30) REVERT: E 242 TYR cc_start: 0.7617 (t80) cc_final: 0.6689 (t80) outliers start: 32 outliers final: 24 residues processed: 214 average time/residue: 0.0642 time to fit residues: 20.7633 Evaluate side-chains 219 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 11 PHE Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 105 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 99 optimal weight: 0.0770 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 0.0870 chunk 106 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 29 optimal weight: 0.0870 chunk 40 optimal weight: 5.9990 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN E 174 GLN E 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.175048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.146023 restraints weight = 16516.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.150913 restraints weight = 10143.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.154354 restraints weight = 7061.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.156796 restraints weight = 5379.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.158411 restraints weight = 4364.100| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10263 Z= 0.126 Angle : 0.665 12.392 14011 Z= 0.328 Chirality : 0.040 0.248 1624 Planarity : 0.004 0.052 1686 Dihedral : 12.565 88.204 1759 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.01 % Allowed : 26.05 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1214 helix: -0.03 (0.18), residues: 793 sheet: None (None), residues: 0 loop : -0.07 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 233 TYR 0.024 0.002 TYR A 194 PHE 0.032 0.002 PHE A 11 TRP 0.036 0.002 TRP E 4 HIS 0.001 0.001 HIS D 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (10261) covalent geometry : angle 0.66490 / 0.33 (14007) SS BOND : bond 0.00097 / 0.05 ( 2) SS BOND : angle 1.43324 / 0.76 ( 4) hydrogen bonds : bond 0.03684 / 2.37 ( 496) hydrogen bonds : angle 4.72303 / 3.25 ( 1434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1373.80 seconds wall clock time: 24 minutes 31.51 seconds (1471.51 seconds total)